You can delete a bond in tleap (deleteBond).
Maria
> On Dec 11, 2021, at 5:21 AM, Aravind R <aradrive1.gmail.com> wrote:
>
> Dear Amber Users,
> I am trying to model a protein with two Zn ions (One coordinated with 4
> CYS whereas the other coordinated with 2 CYS and 2 HIS (one in HIE and one
> in HID protonation states)). I saw that Zn with 4 CYS can be modelled using
> Center ID 1 from ZAFF. The closest I can find for other Zn is Center ID 4.
> when I model the system, tleap throws, lengths, angles & torsions are
> missing for interactions containing two Zn.
> TLEAP SCRIPT:
>
> tleap -s
> source leaprc.protein.ff14SB
> addAtomTypes { { "ZN" "Zn" "sp3" } { "S3" "S" "sp3" } { "N2" "N" "sp3" } }
> loadoff atomic_ions.lib
> source leaprc.water.tip3p
> loadamberprep ZAFF.prep
> loadamberparams ZAFF.frcmod
> x = loadpdb prepped_zaff_named.pdb
> bond x.45.ZN x.3.SG
> bond x.45.ZN x.6.SG
> bond x.45.ZN x.26.SG
> bond x.45.ZN x.29.SG
> bond x.46.ZN x.17.SG
> bond x.46.ZN x.20.SG
> bond x.46.ZN x.35.NE2
> bond x.46.ZN x.38.ND1
> solvatebox x TIP3PBOX 12.0
> addions x NA 0
> savepdb x try_solv.pdb
> saveamberparm x protein.prmtop protein.inpcrd
> quit
>
> ERROR :
> Error: Could not find bond parameter for: ZN - ZN
> Building angle parameters.
>
> Error: Could not find angle parameter: S1 - ZN - ZN
>
> Error: Could not find angle parameter: S1 - ZN - ZN
>
> Error: Could not find angle parameter: S4 - ZN - ZN
>
> Error: Could not find angle parameter: S4 - ZN - N7
>
> Error: Could not find angle parameter: S4 - ZN - ZN
>
> Error: Could not find angle parameter: S4 - ZN - N7
>
> Error: Could not find angle parameter: S1 - ZN - ZN
>
> Error: Could not find angle parameter: S1 - ZN - ZN
>
> Error: Could not find angle parameter: N3 - ZN - ZN
>
> Error: Could not find angle parameter: N3 - ZN - N7
>
> Error: Could not find angle parameter: N7 - ZN - ZN
> Building proper torsion parameters.
>
> Error: ** No torsion terms for S1-ZN-ZN-S4
>
> Error: ** No torsion terms for S1-ZN-ZN-S4
>
> Error: ** No torsion terms for S1-ZN-ZN-N3
>
> Error: ** No torsion terms for S1-ZN-ZN-N7
>
> Error: ** No torsion terms for CT-S1-ZN-ZN
>
> Error: ** No torsion terms for S1-ZN-ZN-S4
>
> Error: ** No torsion terms for S1-ZN-ZN-S4
>
> Error: ** No torsion terms for S1-ZN-ZN-N3
>
> Error: ** No torsion terms for S1-ZN-ZN-N7
>
> Error: ** No torsion terms for CT-S1-ZN-ZN
>
> Error: ** No torsion terms for S4-ZN-ZN-S1
>
> Error: ** No torsion terms for S4-ZN-ZN-S1
>
> Error: ** No torsion terms for S4-ZN-N7-CC
>
> Error: ** No torsion terms for S4-ZN-N7-CR
>
> Error: ** No torsion terms for CT-S4-ZN-ZN
>
> Error: ** No torsion terms for CT-S4-ZN-N7
>
> Error: ** No torsion terms for S4-ZN-ZN-S1
>
> Error: ** No torsion terms for S4-ZN-ZN-S1
>
> Error: ** No torsion terms for S4-ZN-N7-CC
>
> Error: ** No torsion terms for S4-ZN-N7-CR
>
> Error: ** No torsion terms for CT-S4-ZN-ZN
>
> Error: ** No torsion terms for CT-S4-ZN-N7
>
> Error: ** No torsion terms for S1-ZN-ZN-N3
>
> Error: ** No torsion terms for S1-ZN-ZN-N7
>
> Error: ** No torsion terms for CT-S1-ZN-ZN
>
> Error: ** No torsion terms for S1-ZN-ZN-N3
>
> Error: ** No torsion terms for S1-ZN-ZN-N7
>
> Error: ** No torsion terms for CT-S1-ZN-ZN
>
> Error: ** No torsion terms for CV-N3-ZN-ZN
>
> Error: ** No torsion terms for CV-N3-ZN-N7
>
> Error: ** No torsion terms for N3-ZN-N7-CC
>
> Error: ** No torsion terms for N3-ZN-N7-CR
>
> Error: ** No torsion terms for CR-N3-ZN-ZN
>
> Error: ** No torsion terms for CR-N3-ZN-N7
>
> Error: ** No torsion terms for CR-N7-ZN-ZN
>
> Error: ** No torsion terms for CC-N7-ZN-ZN
>
> I two Zn are away and are not bonded. Why is tleap asking for these bonded
> parameters?
> What is the best way to model this system?
> Any help is appreciated.
> Regards,
> Aravind R
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Received on Sun Dec 12 2021 - 17:30:02 PST
